In this study, field trials on fine and coarse spray quality application of pesticides on apples were performed. The main objectives were to study the variation of pesticide residue levels in individual fruits versus composite samples, and the effect of standard fine spray quality application versus coarse spray quality application on residue levels. The applications included boscalid, bupirimate, captan, fenoxycarb, indoxacarb, pirimicarb, pyraclostrobin and thiophanate-methyl. Apples were collected from four zones in the tree and pesticide residues were detected in the individual apples. None of the results for the pesticides residues measured in individual apples exceeded the EU Maximum Residue Levels (MRLs). However, there was a large variation in the residues levels in the apples, with levels from 0.01 to 1.4 mg kg−1 for captan, the pesticide with the highest variation, and from 0.01 to 0.2 mg kg−1 for pyraclostrobin, the pesticide with the lowest variation. Residues of fenoxycarb and indoxacarb were only found in a few apples, probably due to the early application time of these two compounds. The evaluation of the effect of spray quality did not show any major difference between fine and coarse spray quality, except for carbendazim, the degradation product of thiophanate-methyl, where fine spray quality resulted in higher carbendazim residue levels than coarse spray quality. To examine the relationship between individual results and average results from ten apples, 20 composite samples were statistically constructed from sets of ten of the individual results. The variability factors for the individual samples (n = 80) at the 97.5 percentile were calculated for both standard and air induction nozzle application and were in the range of 0.9–9.4. The variability factor of seven used when EU member states calculate possible exceeding of Acute Reference Dose (ARfD) was adequate to encompass almost all the average results from the analyses of ten individual apples. However, for captan up to 9% of the results were not covered depending on which of the mathematically constructed composite concentrations was chosen. The variability factor of three, recommend by Codex, seems to be too low, because up to 30% of the apple samples for captan were not covered if the worst case scenario was chosen. The factor of three seems was also too low for thiophanate-methyl.